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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Thu Dec 23 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Students Experience of Hybrid- Education Model at The University of Baghdad College of Pharmacy
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The impact of COVID-19 pandemic on education models was mainly through the expansion of technology use in the different educational programs. Earlier impact of COVID-19 was manifested in the complete and sudden transition to distance education regardless of institution preparedness status. Gradually, many institutions are moving back to on-campus face-to-face education. However, others including all higher education institutions in Iraq are adopting the hybrid education model. This report presents part of the end of semester evaluation survey conducted at the University of Baghdad College of Pharmacy for the Spring 2021 semester. The survey aims to address points of strength and weakness associated with the hybrid education model and spe

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Publication Date
Fri Nov 11 2022
Journal Name
Surgical Neurology International
Brown-Sequard syndrome associated with a spinal cord injury caused by a retained screwdriver: A case report and literature review
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Background:

Nonmissile penetrating spine injury (NMPSI) represents a small percent of spinal cord injuries (SCIs), estimated at 0.8% in Western countries. Regarding the causes, an NMPSI injury caused by a screwdriver is rare. This study reports a case of a retained double-headed screwdriver in a 37-year-old man who sustained a stab injury to the back of the neck, leaving the patient with a C4 Brown-Sequard syndrome (BSS). We discuss the intricacies of the surgical management of such cases with a literature review.

Methods:

PubMed database was searched by the following combined formula of medical subjects headings,

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Publication Date
Thu Jan 01 2015
Journal Name
Iraqi Postgraduate Medical Journal
Immunohistochemical Study of Leydig Cells in the Testicular Interstitial Tissue of Rats Treated with Tribulus Terrestris Using P450scc.
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BACKGROUND: Tribulus terrestris has been commonly used in folk medicine to energize, vitalize and improve sexual function and physical performance in men and laboratory rats. OBJECTIVE: To study the effect of Tribulus terrestris on the number of Leydig cells. MATERIALS AND METHODS: Tribulus terrestris was given to mature male rats as an oral single herbal suspension in a dose of 2.0mg /1000gbody weight for 14 days to stimulate spermatogenesis. Formalin fixed paraffinembedded tissue sections were performed for histological, immunohistochemical and morphometrical studies. RESULTS: Histological study revealed wider seminiferous tubules and increased spermatocytes population with an increased sperm density inside the lumen of the tubul

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Publication Date
Sun Jun 30 2013
Journal Name
Al-khwarizmi Engineering Journal
Thermodynamic and Kinetic Study of the Adsorption of Pb (II) from Aqueous Solution Using Bentonite and Activated Carbon
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The adsorption of Pb(II) ions onto bentonite and activated carbon was investigated. The effects of pH, initial adsorbent dosage, contact time and temperature were studied in batch experiments. The maximum adsorption capacities for bentonite and activated carbon were 0.0364 and 0.015 mg/mg, respectively. Thermodynamic parameters such as Gibbs free energy change, Enthalpy change and Entropy change have been calculated. These thermodynamic parameters indicated that the adsorption process was thermodynamically spontaneous under natural conditions and the adsorption was endothermic in nature. Experimental data were also tested in terms of adsorption kinetics, the results showed that the adsorption processes followed well pseudo second- order

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Publication Date
Mon Feb 06 2023
Journal Name
Journal Of Toxicology
Zinc Chloride Can Mitigate the Alterations in Metallothionein and Some Apoptotic Proteins Induced by Cadmium Chloride in Mice Hepatocytes: A Histological and Immunohistochemical Study
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The heavy metal cadmium is extremely harmful to both humans and animals. Zinc supplementation protects the biological system and reduces cadmium-induced toxicity. This study aimed to determine whether zinc chloride (ZnCl2) could protect male mice with the damaged liver induced by cadmium chloride (CdCl2). The protective role of zinc chloride and expression of the metallothionein (MT), Ki-67, and Bcl-2 apoptotic proteins in hepatocytes were studied after subchronic exposure of mice to cadmium chloride for 21 days. Thirty male mice were randomly categorized into 6 groups (5 mice/group) as follows: a control group that did not receive any treatment, a group given ZnCl2 at 10 mg/kg alone, and two groups received ZnCl2 (10 mg/kg) i

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Publication Date
Tue May 01 2018
Journal Name
International Journal Of Medical Research & Health Sciences
Estimation of Serum Matrix Metalloproteinases-1 Levels in Iraqi Female Patients with Osteoarthritis
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This study was established to investigate the correlation between the expression of matrix metalloproteinases (MMP-1) and the pathogenesis of osteoarthritis (OA). Blood samples were collected from 55 female patients with inflammatory OA and controls for estimation of serum (MMP-1) levels. In the current study, there is significant increase (p<0.001) in the mean of serum MMP-1 levels in osteoarthritis females (4027.73 ± 1345.28 pg/ml) than that in control females (798.76 ± 136.79 pg/ml). It was concluded that MMP-1 may be associated with the pathogenesis of osteoarthritis.

Publication Date
Wed May 12 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Role of Serum Omentin-1 and Bone Metabolism Markersin Osteoporosis among Postmenopausal Women
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menopause is the most common cause of accelerated bone loss in women. Omentin-1 is secreted by the visceral adipose tissue and it isdonated in the regulation of bone metabolism in postmenopausal women which is related with decreased bone mineral density. The current study aims to investigate the role of serum omentin-1and some bone metabolism markers in osteoporosis among postmenopausal Iraqi women. This study was performedin the Rheumatology and Rehabilitation Unit, Baghdad Teaching Hospital/ Baghdad medical city, during the period from November 2019 to July 2020 with a total of 60 postmenopausal women(30 with osteoporosis and 30 without osteoporosis), their ages ranged from 52 to 62 years. They were compared with 30 healthy premenopausal

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Publication Date
Wed Jan 01 2020
Journal Name
American Journal Of Dermatology And Venereology
Intralesional Therapy of Vitiligo by 1% Lactic Acid Solution Versus Triamcinolone Acetonide Injection
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KE Sharquie, AA Noaimi, S Adnan, AM Al-Niddawi, WK Aljanabi, American Journal of Dermatology and Venereology, 2020 - Cited by 2

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Publication Date
Wed May 13 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Immunoflourescent assessment of Herpes Simplex Virus (HSV) type 1 in oral lichen planus
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Background: Oral lichen planus is one of the most common dermatological diseases presenting in the oral cavity. Hence, viral infection of the oral mucosa may be involved in the pathogenesis of oral lichen planus, Taking in to consideration the oncogenic potential of HSV-1, this study aimed to assess the presence of Herpes Simplex Virus type one by direct immunoflourescent in oral lichen planus. This study aimed to assess the presence of HSV type1 by direct immunofluorescent in histopathologically diagnosed OLP Material and Method: Twenty formalin fixed embedded tissue blocks of oral lichen planus with 2 Positive control cases were taken from patients having infection with herpes labialis, US Biological herpes simplex virus-1 Glycoprotein

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Publication Date
Tue Jan 01 2019
Journal Name
Annals Of Tropical Medicine And Public Health
Arlyesterase activity of Paraoxonase-1 enzyme in Iraqi patients with β-thalassemia minor
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Background: Arylesterase activity of Paraoxonase-1 (ARE-PON-1) exhibits an antioxidant role which protects lipoprotein from oxidation. It is known that ARE-PON-1 antioxidant activity associated with high density lipoprotein cholesterol (HDL-C) reduces the oxidative damage mediated by low density lipoprotein cholesterol (LDL-C). The present study was aimed to examine the level of serum ARE-PON1 in Iraqi patients with β-thalassemia minor and its relationship with lipid profile (total cholesterol (TC), HDL-C, very low density lipoprotein (VLDL-C), and LDL-C) and hematologic changes as a part of antioxidant system action. Methods: In the present study, the ARE-PON-1 activity was investigated in serum of patients with β-thalassemia minor. Resu

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